Genome-wide identification, phylogeny and expression analyses of SCARECROW-LIKE(SCL) genes in millet (Setaria italica)
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As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6–8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis, maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis-elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C4 photosynthesis and bioenergy studies.
KeywordsSetaria italica GRAS family SCARECROW-LIKE (SCL) genes Bioinformatics Gene expression patterns
We thank the Natural Science Foundation of Hebei Province (No. C2015201176), the Scientific Research Foundation for the Returned Overseas Chinese Scholars by State Education Ministry of China (No. 2011–1139), the Postgraduate Research Innovation Fund Project of Hebei Province (S201622) for funding.
HL performed the experiments, analyzed the data and wrote the manuscript; JQ, HF, JC, LL participated in analyzing data; ZL conceived the study, analyzed the data and revised the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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